Abstract: In the present study, 41cp genomes of Magnoliaceae species were used to determine the phylogenetic relationship. Results showed that the cp genomes of tested species were significantly variable at genome size (142723-160183 bp) and gene contents (116-138 genes). Three phylogenetic trees were constructed based on the whole chloroplast genome sequences (WCGS), coding sequences (CDS) and matK gene sequences, respectively. It is demonstrated that the three methods had consistent clustering results of the well-defined Magnoliaceae species, supporting the conclusion of traditional morphological classification. And the phylogenetic tree constructed based on WCGS had the highest bootstrap values (BVs), thus, the phylogenetic relationship was likely more appropriate to reveal the evolutionary process. Based on WCGS phylogenetic trees, the Liriodendron genus had a closed relationship to Magnolioideae species. Among these Magnolioideae species, Magnolia odoratissima showed a relatively distant relationship to other species. Our study clarified the appropriate methods for phylogenetic analysis of Magnoliaceae species, and constructed the phylogenetic relationship among selected Magnoliaceae species at chloroplast DNA level, which could be benefit to accurate identification and genetic resources conservation of Magnoliaceae species.

Key words: Magnoliaceae, Magnolioideae, chloroplast genome, phylogenetic analysis